FIJI (ImageJ): Stack Alignment & Image Registration [SIFT]
ฝัง
- เผยแพร่เมื่อ 28 ก.ย. 2024
- Learn how to use FIJI (ImageJ) to align image stacks (z or time) using the SIFT algorithm. This is one of the plugins for image Registration. SIFT (Scale-Invariant Feature Transform) is an algorithm developed by David Lowe and is used for image alignment and object recognition. The robustness of this method enables detection of features at different scales, angles and illumination of a scene. The SIFT MultiChannel Align plugin, available via the PTBIOP update site, extends the SIFT algorithm to multichannel image stacks.
Plugin Authors:
Linear Stack Alignment with SIFT: Stephan Saalfeld
The EPFL - PTBIOP (BioImaging & Optics Platform) Update Site,
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Hello, when I apply this on a hyperstack the entire frame shifts. I am trying to fix a constant heartbeat in my data. Any tips
Hi! I don’t think the SIFT plugin works on hyperstacks of z and t if this is what you have. Which do you need to align - z or time? On the other hand, if you have a multi-channel time series, you might need to adjust some of the registration parameters or select a different transformation algorithm.
Hello. Thank you for your video. Do you have any video that show how to turn images stack into 3D image? And can I do the alignment to get rid of the drift before turning it into 3D?
@@TNTT1234 Hello! Thanks for watching. You can check out these videos for creating a stack from a sequence of images and doing a 3D reconstruction:
th-cam.com/video/_D1kbKjZtjk/w-d-xo.htmlsi=qNwIhuYjzaj0KEM-
th-cam.com/video/i-Ta4vCRW2s/w-d-xo.htmlsi=pHjihABbx4elO39E
You can also try 3D Script:
th-cam.com/video/Zcb0hhZsYqU/w-d-xo.htmlsi=ZXyjb9FVpD2wLpR-
For image registration, you can do this once you have a stack of images and before 3D rendering.
@@johanna.m.dela-cruz thank you so much. I am appreciated.
Great video! Thanks Johanna!!!!!!
Thank you, Luca. You just made my day.
Hey, im having trouble finding the .jave file for SIFT/ am new to ImajeJ. Any tips on installing the plug-in would be much appreciated! thanks
Hi Dylan. SIFT is bundled with Fiji, so I suggest that you download Fiji. You can download it here: fiji.sc
Hi, i am trying to track rod-shaped cells moving with high speed by FIJI(ImageJ),but i found the plugin only works for Single Particles or Spot-like Objects, could you make a video to teach me how to track the rod-shaped cells please? i would really appreciate that. Thank you!
Hi @joy ye. Thanks for reaching out. I did see your comment earlier on my tracking video. I’ll work on this.
@@johanna.m.dela-cruz Thank you, you are so nice!😘
Hi Johanna, great tutorial! Does the SIFT multichannel tool aligned the shift between channels? Also do you know if there is a way to align z-axis? For example I want all the stacks have highest intensity at slice 20.
Hi there. Thanks for your comment. SIFT multichannel aligns shifts between channels. The registration is based on a particular channel and applies transformation on the other channels. There are other built-in image registration plugins in Fiji. StackReg is also a good choice. I can't quite understand what you mean by all slices having highest intensity at a particular slice.
@@johanna.m.dela-cruz Thanks for the reply. Please let me make an example: If I take a mosaic stack acquisition on a microscope, sometimes the drift doesn't only happen in the xy-axis, but also the z-axis (axial movement). The tutorial fixes the xy drift. Is there a way to align the z drift for 3D stacks? Thanks again
@@axiemetafrontiers5276 You can try StackReg if you only have a shift in z. Correct 3D Drift is used for timelapse images (with z stacks). SIFT Multichannel should work as well.
@@johanna.m.dela-cruz could you suggest a tool to do this? Or SIFT would also be able to do this?
@@axiemetafrontiers5276 Try Correct 3D Drift.